Despite significant advances in the era of highly active anti-retroviral therapy, central nervous system (CNS) effects of human immunodeficiency virus (HIV) have remained prevalent. In this light, we continue to search for sensitive, non-invasive biomarkers to guide treatment, monitor therapeutic intervention, and identify individuals at risk for CNS decline. Previous work has supported the value of neuroimaging for identifying biomarkers in HIV, particularly in the white matter and caudate nucleus. Recent clinical neuroimaging efforts within the multi-site CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) program have employed multiple modalities including structural and diffusion tensor MR imaging to assess the brain's response to HIV infection. CHARTER has employed multi-channel MRI (T1, T2, PD) to produce tissue segmentations with manual delineation of global regions, resulting in successful identification of neuroimaging correlates of HIV, such as abnormalities in the white matter (AbWM). Manual delineation of individual structures (e.g., caudate), however, is prohibitive on large-scale studies. Recent methodological advancements offer promise for automating regional delineation, however, these methods have not yet been validated in HIV. The reliance of these methods solely on T1 sequences can result in the misclassification of AbWM as gray matter, leading to decreased sensitivity and errors in structural volume estimates. Such classification errors may result in systematic bias, due to the correlation of AbWM with disease severity. Utilizing data from CHARTER, we propose to critically assess the performance of two relatively automated subcortical labeling methods in HIV and to examine a statistical pre-processing procedure that may enhance performance of these methods. In particular, we will examine the degree to which HIV-related AbWM affects method performance relative to a morphometric "gold standard." The gold standard regions of interest (e.g., caudate) will be defined upon existing CHARTER morphometry, thus increasing the reliability of the manual delineations. We also will investigate the value of statistically enhancing the input T1 volumes, with information from PD, T2, and diffusion tensor imaging (DTI) volumes, through the use of alternating conditional expectations (ACE), which will use the supplemental volumes to enhance tissue contrast in the T1 volumes. Further validation efforts will examine the relationship between resultant structural volumes and neurobehavioral and medical biomarkers. The systematic assessment and enhancement of structural neuroimaging methodology will allow us to better characterize the underlying neuropathogenesis of HIV, to potentially validate these tools for use in HIV, to provide guidance to end-users, and to offer insight to developers for future work. Importantly, this work will provide regional morphometric data to the CHARTER as a Resource initiative for the exploration of additional, more specific hypothesis testing, such as the value of caudate volume as a biomarker of HIV-related cognitive decline, risk for decline, or effectiveness of therapeutic intervention. PUBLIC HEALTH RELEVANCE: Despite significant advances in the era of highly active anti-retroviral therapy, central nervous system (CNS) effects of human immunodeficiency virus (HIV) have remained prevalent, and the impact of neurological impairment and neurocognitive dysfunction on individuals daily lives, work performance, and care needs can be significant. The on-going multi-site CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) program provides a unique multidisciplinary setting for the characterization of such effects, within which we propose a systematic assessment and enhancement of structural neuroimaging methods, not previously validated in HIV. This work will provide regional morphometric data to the CHARTER as a Resource initiative for the exploration of additional, more specific neuroimaging correlates of HIV to guide treatment, monitor therapeutic intervention, and identify individuals at risk for CNS decline.